At the moment, BIDS session paths are resolved using the absolute path of the BIDS directory inside a running Docker container. This means that, whether or not the session paths actually correspond to their real paths on the host FS where the CLI was run, depends on whether the user has mounted the BIDS directory to the same absolute location in the CLI container as the host (example commands provided in our docs do this by default).
More advanced users may choose to mount paths differently when running the CLI, resulting in non-existent session paths in the JSONLD file.
To avoid this issue, we can add an argument for the user to specify explicitly the absolute path to the BIDS directory root.
At the moment, BIDS session paths are resolved using the absolute path of the BIDS directory inside a running Docker container. This means that, whether or not the session paths actually correspond to their real paths on the host FS where the CLI was run, depends on whether the user has mounted the BIDS directory to the same absolute location in the CLI container as the host (example commands provided in our docs do this by default).
More advanced users may choose to mount paths differently when running the CLI, resulting in non-existent session paths in the JSONLD file.
To avoid this issue, we can add an argument for the user to specify explicitly the absolute path to the BIDS directory root.